Oak bacterial and fungal isolates obtained by agar plating under growth conditions targeting stem microbiota. (A) Comparison of the number of bacterial isolates and ASVs obtained in a combination of five growth media (NtA, MEA, PGA, R2A, and TSA) under aerobic incubation and with inoculation of stem cell suspensions and stem pieces vs a combination of six growth media (addition of FAA agar) under anaerobic conditions, and with inoculation of stem cell suspensions and stem pieces, (B) taxonomic composition of bacterial isolates, (C) number of fungal isolates and ASVs obtained under aerobic conditions using the growth media and sample inoculations described above, (D) taxonomic composition of fungal isolates. Isolates obtained in a combination of five or six growth media were pooled and the number of ASVs and taxonomic composition of the isolates was determined by single-gene profiling of the 16S rRNA gene, for bacterial isolates, and the ITS, for fungal isolates. The number of ASVs per each bacterial and fungal genus was calculated and the proportion of ASVs per genus is displayed in stacked bar plots (C and D). The growth media used were MEA, NtA, PGA, TSA, R2A, and FAA.